We recommend to find an accommodation in the city center. The city center is the yellow area in Google Maps: from Piazza Vittorio Emanuele up to Ponte di Mezzo, and after Ponte di Mezzo until Piazza del Duomo on one side, and the Department of Computer Science (Dipartimento di Informatica) on the other side. Avoid the railway station area, although safe, it is not so nice.
From the city center, you can walk to CNR (around 25 mins). There are also buses connecting the city center with the CNR premises. The best choice is LAM Verde, which stops at the railway station and also along the Arno river in the city center. Check connections in Google Maps.
Below is a list of suggested Hotels in Pisa.
Hotel Bologna **** (2.5 Km/30 mins walking)
Hotel di Stefano *** (2.1 Km/26 mins walking)
Hotel Minerva *** (2.1 Km/26 mins walking)
Hotel Alessandro della Spina *** (2.4 Km/30 min walking)
Hotel Repubblica Marinara **** (1.3 Km/16 mins walking)
Hotel Verdi*** (1.6 Km/20 mins walking)
Hotel Royal Victoria *** (2.1 Km walking/25 mins)